public clsCorrelation(clsBinningOptions binningOptions)
{
mBinningOptions = binningOptions;
NoiseThresholdIntensity = 0;
mCoefficients = new[] { 76.180091729471457, -86.505320329416776,
24.014098240830911, -1.231739572450155,
0.001208650973866179, -0.000005395239384953 };
}
private float CompareSpectra(
clsMSSpectrum fragSpectrum1,
clsMSSpectrum fragSpectrum2,
clsBinningOptions binningOptions,
bool considerOffsetBinnedData = true)
{
// Compares the two spectra and returns a similarity score (ranging from 0 to 1)
// Perfect match is 1; no similarity is 0
// Note that both the standard binned data and the offset binned data are compared
// If considerOffsetBinnedData = True, then the larger of the two scores is returned
// similarity scores is returned
//
// If an error, returns -1
var binnedSpectrum1 = new clsBinnedData();
var binnedSpectrum2 = new clsBinnedData();
try
{
var dataComparer = new clsCorrelation(binningOptions);
RegisterEvents(dataComparer);
const clsCorrelation.cmCorrelationMethodConstants eCorrelationMethod = clsCorrelation.cmCorrelationMethodConstants.Pearson;
// Bin the data in the first spectrum
var success = CompareSpectraBinData(dataComparer, fragSpectrum1, binnedSpectrum1);
if (!success)
{
return(-1);
}
// Bin the data in the second spectrum
success = CompareSpectraBinData(dataComparer, fragSpectrum2, binnedSpectrum2);
if (!success)
{
return(-1);
}
// Now compare the binned spectra
// Similarity will be 0 if either instance of BinnedIntensities has fewer than 5 data points
var similarity1 = dataComparer.Correlate(binnedSpectrum1.BinnedIntensities, binnedSpectrum2.BinnedIntensities, eCorrelationMethod);
if (!considerOffsetBinnedData)
{
return(similarity1);
}
var similarity2 = dataComparer.Correlate(binnedSpectrum1.BinnedIntensitiesOffset, binnedSpectrum2.BinnedIntensitiesOffset, eCorrelationMethod);
return(Math.Max(similarity1, similarity2));
}
catch (Exception ex)
{
ReportError("CompareSpectra: " + ex.Message, ex);
return(-1);
}
}
private float CompareFragSpectraForParentIons(
clsScanList scanList,
clsSpectraCache spectraCache,
int parentIonIndex1,
int parentIonIndex2,
clsBinningOptions binningOptions,
MASICPeakFinder.clsBaselineNoiseOptions noiseThresholdOptions,
DataInput.clsDataImport dataImportUtilities)
{
// Compare the fragmentation spectra for the two parent ions
// Returns the highest similarity score (ranging from 0 to 1)
// Returns 0 if no similarity or no spectra to compare
// Returns -1 if an error
float highestSimilarityScore;
try
{
if (scanList.ParentIons[parentIonIndex1].CustomSICPeak || scanList.ParentIons[parentIonIndex2].CustomSICPeak)
{
// Custom SIC values do not have fragmentation spectra; nothing to compare
highestSimilarityScore = 0;
}
else if (scanList.ParentIons[parentIonIndex1].MRMDaughterMZ > 0 || scanList.ParentIons[parentIonIndex2].MRMDaughterMZ > 0)
{
// MRM Spectra should not be compared
highestSimilarityScore = 0;
}
else
{
highestSimilarityScore = 0;
foreach (var fragSpectrumIndex1 in scanList.ParentIons[parentIonIndex1].FragScanIndices)
{
if (!spectraCache.GetSpectrum(scanList.FragScans[fragSpectrumIndex1].ScanNumber, out var spectrum1, false))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return(-1);
}
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
if (!clsMASIC.DISCARD_LOW_INTENSITY_MSMS_DATA_ON_LOAD)
#pragma warning disable 162
// ReSharper disable HeuristicUnreachableCode
{
dataImportUtilities.DiscardDataBelowNoiseThreshold(spectrum1, scanList.FragScans[fragSpectrumIndex1].BaselineNoiseStats.NoiseLevel, 0, 0, noiseThresholdOptions);
}
// ReSharper restore HeuristicUnreachableCode
#pragma warning restore 162
foreach (var fragSpectrumIndex2 in scanList.ParentIons[parentIonIndex2].FragScanIndices)
{
if (!spectraCache.GetSpectrum(scanList.FragScans[fragSpectrumIndex2].ScanNumber, out var spectrum2, false))
{
SetLocalErrorCode(clsMASIC.eMasicErrorCodes.ErrorUncachingSpectrum);
return(-1);
}
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
if (!clsMASIC.DISCARD_LOW_INTENSITY_MSMS_DATA_ON_LOAD)
#pragma warning disable 162
// ReSharper disable HeuristicUnreachableCode
{
dataImportUtilities.DiscardDataBelowNoiseThreshold(spectrum2, scanList.FragScans[fragSpectrumIndex2].BaselineNoiseStats.NoiseLevel, 0, 0, noiseThresholdOptions);
}
// ReSharper restore HeuristicUnreachableCode
#pragma warning restore 162
var similarityScore = CompareSpectra(spectrum1, spectrum2, binningOptions);
if (similarityScore > highestSimilarityScore)
{
highestSimilarityScore = similarityScore;
}
}
}
}
}
catch (Exception ex)
{
ReportError("Error in CompareFragSpectraForParentIons", ex);
return(-1);
}
return(highestSimilarityScore);
}
